https://www.alphaknockout.com
Mouse Bicd1 Knockout Project (CRISPR/Cas9)
Objective: To create a Bicd1 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Bicd1 gene (NCBI Reference Sequence: NM_009753 ; Ensembl: ENSMUSG00000003452 ) is located on Mouse chromosome 6. 9 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 8 (Transcript: ENSMUST00000086829). Exon 4~6 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note:
Exon 4 starts from about 23.15% of the coding region. Exon 4~6 covers 66.79% of the coding region. The size of effective KO region: ~5393 bp. The KO region does not have any other known gene.
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Overview of the Targeting Strategy
Wildtype allele 5' gRNA region gRNA region 3'
1 4 5 6 9
Legends Exon of mouse Bicd1 Knockout region
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Overview of the Dot Plot (up) Window size: 15 bp
Forward Reverse Complement
Sequence 12
Note: The 2000 bp section upstream of Exon 4 is aligned with itself to determine if there are tandem repeats. Tandem repeats are found in the dot plot matrix. The gRNA site is selected outside of these tandem repeats.
Overview of the Dot Plot (down) Window size: 15 bp
Forward Reverse Complement
Sequence 12
Note: The 1821 bp section downstream of Exon 6 is aligned with itself to determine if there are tandem repeats. Tandem repeats are found in the dot plot matrix. The gRNA site is selected outside of these tandem repeats.
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Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(32.05% 641) | C(15.4% 308) | T(36.75% 735) | G(15.8% 316)
Note: The 2000 bp section upstream of Exon 4 is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis.
Overview of the GC Content Distribution (down) Window size: 300 bp
Sequence 12
Summary: Full Length(1821bp) | A(32.07% 584) | C(15.93% 290) | T(36.13% 658) | G(15.87% 289)
Note: The 1821 bp section downstream of Exon 6 is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis.
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BLAT Search Results (up)
QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ------browser details YourSeq 2000 1 2000 2000 100.0% chr6 + 149509693 149511692 2000 browser details YourSeq 172 881 1246 2000 87.7% chr1 + 155374857 155550541 175685 browser details YourSeq 139 962 1245 2000 79.8% chr10 + 30168722 30168966 245 browser details YourSeq 138 990 1245 2000 86.3% chr4 + 143715791 143716168 378 browser details YourSeq 122 1088 1290 2000 84.4% chr2 - 26274179 26274380 202 browser details YourSeq 120 1089 1245 2000 88.4% chrX + 90350637 90350802 166 browser details YourSeq 119 894 1250 2000 76.3% chr6 + 119283703 119283883 181 browser details YourSeq 119 1097 1253 2000 89.1% chr2 + 90899527 91310729 411203 browser details YourSeq 119 983 1242 2000 85.7% chr13 + 65759682 65759943 262 browser details YourSeq 118 1088 1245 2000 87.4% chr8 + 45566754 45566911 158 browser details YourSeq 117 1087 1245 2000 87.1% chr3 - 10299054 10299228 175 browser details YourSeq 117 886 1245 2000 76.3% chrX + 162627534 162627699 166 browser details YourSeq 117 1087 1253 2000 86.0% chr9 + 119693590 119693757 168 browser details YourSeq 116 995 1237 2000 81.3% chr19 - 45776472 45776651 180 browser details YourSeq 116 1084 1246 2000 83.2% chr1 + 32378829 32378988 160 browser details YourSeq 114 1087 1245 2000 87.5% chr14 - 124437081 124437241 161 browser details YourSeq 114 1084 1253 2000 85.2% chr1 - 110354664 110354839 176 browser details YourSeq 112 990 1244 2000 84.2% chr12 - 4056081 4056453 373 browser details YourSeq 112 990 1240 2000 85.4% chr7 + 126934516 126935051 536 browser details YourSeq 111 1086 1253 2000 86.8% chr17 + 29239826 29239991 166
Note: The 2000 bp section upstream of Exon 4 is BLAT searched against the genome. No significant similarity is found.
BLAT Search Results (down)
QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ------browser details YourSeq 1821 1 1821 1821 100.0% chr6 + 149517086 149518906 1821 browser details YourSeq 44 683 1032 1821 70.0% chr10 + 86985195 86985481 287 browser details YourSeq 41 1043 1348 1821 91.9% chr4 + 106766125 106766432 308 browser details YourSeq 38 709 1008 1821 58.0% chr19 + 59764972 59765140 169 browser details YourSeq 37 253 290 1821 100.0% chr14 + 115996876 115996914 39 browser details YourSeq 28 681 714 1821 86.7% chr11 - 119568121 119568152 32 browser details YourSeq 27 1676 1733 1821 96.6% chr2 + 113834752 113834809 58 browser details YourSeq 24 690 715 1821 96.2% chr7 - 97040866 97040891 26 browser details YourSeq 24 250 273 1821 100.0% chr3 - 33741388 33741411 24 browser details YourSeq 24 684 713 1821 77.8% chr13 + 102350011 102350037 27 browser details YourSeq 20 694 713 1821 100.0% chr15 - 62153027 62153046 20
Note: The 1821 bp section downstream of Exon 6 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Bicd1 BICD cargo adaptor 1 [ Mus musculus (house mouse) ] Gene ID: 12121, updated on 12-Aug-2019
Gene summary
Official Symbol Bicd1 provided by MGI Official Full Name BICD cargo adaptor 1 provided by MGI Primary source MGI:MGI:1101760 See related Ensembl:ENSMUSG00000003452 Gene type protein coding RefSeq status VALIDATED Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as bic-D 1; B830009D06Rik Expression Broad expression in cerebellum adult (RPKM 3.4), CNS E18 (RPKM 3.2) and 17 other tissues See more Orthologs human all
Genomic context
Location: 6; 6 G3 See Bicd1 in Genome Data Viewer Exon count: 11
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (149408824..149563329)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 6 NC_000072.5 (149357408..149507379)
Chromosome 6 - NC_000072.6
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Transcript information: This gene has 9 transcripts
Gene: Bicd1 ENSMUSG00000003452
Description BICD cargo adaptor 1 [Source:MGI Symbol;Acc:MGI:1101760] Gene Synonyms B830009D06Rik Location Chromosome 6: 149,408,886-149,563,329 forward strand. GRCm38:CM000999.2 About this gene This gene has 9 transcripts (splice variants), 251 orthologues, 1 paralogue, is a member of 1 Ensembl protein family and is associated with 8 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Bicd1- ENSMUST00000086829.10 9667 835aa ENSMUSP00000084039.4 Protein coding CCDS39723 Q8BR07 TSL:1 202 GENCODE basic APPRIS P2
Bicd1- ENSMUST00000111513.8 4049 826aa ENSMUSP00000107138.2 Protein coding CCDS51962 Q8BR07 TSL:1 203 GENCODE basic
Bicd1- ENSMUST00000003544.13 2928 975aa ENSMUSP00000003544.7 Protein coding - B2KG46 TSL:5 201 GENCODE basic APPRIS ALT1
Bicd1- ENSMUST00000172926.1 413 137aa ENSMUSP00000133986.1 Protein coding - G3UY88 CDS 5' and 3' 206 incomplete TSL:5
Bicd1- ENSMUST00000173408.7 2818 827aa ENSMUSP00000133727.1 Nonsense mediated - G3UXK5 TSL:5 207 decay
Bicd1- ENSMUST00000203502.1 10443 No - Retained intron - - TSL:NA 209 protein
Bicd1- ENSMUST00000140759.2 6758 No - Retained intron - - TSL:1 205 protein
Bicd1- ENSMUST00000130270.1 3998 No - Retained intron - - TSL:1 204 protein
Bicd1- ENSMUST00000174886.1 621 No - Retained intron - - TSL:3 208 protein
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174.44 kb Forward strand 149.40Mb 149.45Mb 149.50Mb 149.55Mb Genes (Comprehensive set... Gm15786-201 >processed pseudogene Bicd1-208 >retained intron Bicd1-205 >retained intron
Gm15783-201 >processed pseudogene Bicd1-206 >protein coding Gm21814-202 >lncRNA
Bicd1-209 >retained intron Gm21814-203 >lncRNA
Bicd1-202 >protein coding
Bicd1-203 >protein coding
Bicd1-204 >retained intron Gm44043-201 >TEC
Bicd1-207 >nonsense mediated decay
Bicd1-201 >protein coding
Contigs < AC163647.3 < AC164090.3 Genes < Gm15785-201processed pseudogene (Comprehensive set...
Regulatory Build
149.40Mb 149.45Mb 149.50Mb 149.55Mb Reverse strand 174.44 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
Ensembl protein coding merged Ensembl/Havana
Non-Protein Coding
RNA gene processed transcript pseudogene
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Transcript: ENSMUST00000086829
154.35 kb Forward strand
Bicd1-202 >protein coding
ENSMUSP00000084... PDB-ENSP mappings MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Pfam Bicaudal-D protein PANTHER Bicaudal-D protein
PTHR31233:SF3
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant synonymous variant
Scale bar 0 80 160 240 320 400 480 560 640 720 835
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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